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The Role Of Software Engineering In Bioinformatics
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1 of the 129 references listed on this page is in the Retraction Watch database as retracted (export 2026-10-28): 10.1038/nm1491 (notice 2011-01-07).
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/0471028959.sof589openalex-snapshot
Capability Maturity Model for Software
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Software configuration management for the 21st century
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Make — a program for maintaining computer programs
inferredcites →https://doi.org/10.1006/geno.1996.0614openalex-snapshot
Sensitivity and Selectivity in Protein Similarity Searches: A Comparison of Smith–Waterman in Hardware to BLAST and FASTA
inferredcites →https://doi.org/10.1007/11535294_25openalex-snapshot
RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs
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Using Docker Containers to Improve Reproducibility in Software and Web Engineering Research
inferredcites →https://doi.org/10.1007/978-3-319-50070-6_4openalex-snapshot
Visualizing Next-Generation Sequencing Cancer Data Sets with Cloud Computing
inferredcites →https://doi.org/10.1007/978-3-642-03770-2_9openalex-snapshot
MPI on a Million Processors
inferredcites →https://doi.org/10.1007/978-3-642-21437-0_7openalex-snapshot
TraceContract: A Scala DSL for Trace Analysis
inferredcites →https://doi.org/10.1007/978-3-642-33666-9_21openalex-snapshot
The Coroutine Model of Computation
inferredcites →https://doi.org/10.1007/978-3-662-09507-2_10openalex-snapshot
Can Programming Be Liberated from the Von Neumann Style? A Functional Style and its Algebra of Programs
inferredcites →https://doi.org/10.1007/s10096-018-3296-5openalex-snapshot
Antimicrobial resistance and molecular epidemiology using whole-genome sequencing of Neisseria gonorrhoeae in Ireland, 2014–2016: focus on extended-spectrum cephalosporins and azithromycin
inferredcites →https://doi.org/10.1007/s11227-011-0656-7openalex-snapshot
StreamPI: a stream-parallel programming extension for object-oriented programming languages
inferredcites →https://doi.org/10.1016/0010-4825(78)90032-xopenalex-snapshot
Interactive instruction on population interactions
inferredcites →https://doi.org/10.1016/0196-8858(81)90046-4openalex-snapshot
Comparison of biosequences
inferredcites →https://doi.org/10.1016/j.cell.2019.02.003openalex-snapshot
Genomic Medicine–Progress, Pitfalls, and Promise
inferredcites →https://doi.org/10.1016/j.cell.2019.02.032openalex-snapshot
Genomic Analysis in the Age of Human Genome Sequencing
inferredcites →https://doi.org/10.1016/j.cels.2018.03.014openalex-snapshot
Practical Computational Reproducibility in the Life Sciences
inferredcites →https://doi.org/10.1016/j.compbiomed.2013.09.011openalex-snapshot
Accelerating in silico research with workflows: A lesson in Simplicity
inferredcites →https://doi.org/10.1016/j.ijinfomgt.2014.10.007openalex-snapshot
Beyond the hype: Big data concepts, methods, and analytics
inferredcites →https://doi.org/10.1016/j.infsof.2008.01.006openalex-snapshot
Empirical studies of agile software development: A systematic review
inferredcites →https://doi.org/10.1016/j.infsof.2012.08.013openalex-snapshot
Design of an empirical study for comparing the usability of concurrent programming languages
inferredcites →https://doi.org/10.1016/j.infsof.2015.07.011openalex-snapshot
Claims about the use of software engineering practices in science: A systematic literature review
inferredcites →https://doi.org/10.1016/j.jbi.2015.01.008openalex-snapshot
HBLAST: Parallelised sequence similarity – A Hadoop MapReducable basic local alignment search tool
inferredcites →https://doi.org/10.1016/j.jpdc.2004.03.006openalex-snapshot
Performance and modularity benefits of message-driven execution
inferredcites →https://doi.org/10.1016/j.mib.2015.06.004openalex-snapshot
The principles of whole-cell modeling
inferredcites →https://doi.org/10.1016/j.tcs.2008.09.019openalex-snapshot
Scala Actors: Unifying thread-based and event-based programming
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1017/s095679689700261xopenalex-snapshot
A foundation for actor computation
inferredcites →https://doi.org/10.1021/ci050126lopenalex-snapshot
Parallelizing a Molecular Dynamics Algorithm on a Multiprocessor Workstation Using OpenMP
inferredcites →https://doi.org/10.1023/b:ijpp.0000029272.69895.c1openalex-snapshot
High Performance RDMA-Based MPI Implementation over InfiniBand
inferredcites →https://doi.org/10.1038/nbt.3780openalex-snapshot
Reproducibility of computational workflows is automated using continuous analysis
inferredcites →https://doi.org/10.1038/ng.295openalex-snapshot
Repeatability of published microarray gene expression analyses
inferredcites →https://doi.org/10.1038/nm1491openalex-snapshot
Genomic signatures to guide the use of chemotherapeutics
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
inferredcites →https://doi.org/10.1038/nrg2048openalex-snapshot
Beyond standardization: dynamic software infrastructures for systems biology
inferredcites →https://doi.org/10.1038/s41436-019-0618-7openalex-snapshot
The complete costs of genome sequencing: a microcosting study in cancer and rare diseases from a single center in the United Kingdom
inferredcites →https://doi.org/10.1073/pnas.48.4.582openalex-snapshot
ON THE GENETIC BASIS OF VARIATION AND HETEROGENEITY OF DNA BASE COMPOSITION
inferredcites →https://doi.org/10.1080/03043798808939429openalex-snapshot
Toward a Definition of the Engineering Method
inferredcites →https://doi.org/10.1080/14636778.2013.773172openalex-snapshot
Inscribing a discipline: tensions in the field of bioinformatics
inferredcites →https://doi.org/10.1080/21655979.2015.1050162openalex-snapshot
Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software
inferredcites →https://doi.org/10.1093/bioinformatics/btl446openalex-snapshot
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
inferredcites →https://doi.org/10.1093/bioinformatics/btx192openalex-snapshot
BioContainers: an open-source and community-driven framework for software standardization
inferredcites →https://doi.org/10.1093/bioinformatics/btx554openalex-snapshot
Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses
inferredcites →https://doi.org/10.1093/biosci/bix034openalex-snapshot
Peer Review: A System under Stress
inferredcites →https://doi.org/10.1093/comjnl/32.2.175openalex-snapshot
Parallel Implementations of Functional Programming Languages
inferredcites →https://doi.org/10.1093/comjnl/32.2.98openalex-snapshot
Why Functional Programming Matters
inferredcites →https://doi.org/10.1093/gigascience/giaa063openalex-snapshot
The democratization of bioinformatics: A software engineering perspective
inferredcites →https://doi.org/10.1093/gigascience/giy036openalex-snapshot
Field of genes: using Apache Kafka as a bioinformatic data repository
inferredcites →https://doi.org/10.1093/nar/gki025openalex-snapshot
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
inferredcites →https://doi.org/10.1093/nar/gku1196openalex-snapshot
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
inferredcites →https://doi.org/10.1093/nsr/nwv042openalex-snapshot
How functional programming mattered
inferredcites →https://doi.org/10.1101/321919openalex-snapshot
A large-scale analysis of bioinformatics code on GitHub
inferredcites →https://doi.org/10.1109/6.591665openalex-snapshot
Moore's law: past, present and future
inferredcites →https://doi.org/10.1109/99.660313openalex-snapshot
OpenMP: an industry standard API for shared-memory programming
inferredcites →https://doi.org/10.1109/bibm.2017.8217980openalex-snapshot
A metagenomics analysis of rumen microbiome
inferredcites →https://doi.org/10.1109/bibm.2018.8621354openalex-snapshot
ImmunoAdept – bringing blood microbiome profiling to the clinical practice
inferredcites →https://doi.org/10.1109/concapan.2017.8278488openalex-snapshot
Refactoring improving the design of existing code
inferredcites →https://doi.org/10.1109/cseet.2009.44openalex-snapshot
Software Engineering Education for Bioinformatics
inferredcites →https://doi.org/10.1109/escience.2008.62openalex-snapshot
CloudBLAST: Combining MapReduce and Virtualization on Distributed Resources for Bioinformatics Applications
inferredcites →https://doi.org/10.1109/esem.2017.11openalex-snapshot
Automatic Building of Java Projects in Software Repositories: A Study on Feasibility and Challenges
inferredcites →https://doi.org/10.1109/icccbda.2016.7529531openalex-snapshot
Big data stream computing in healthcare real-time analytics
inferredcites →https://doi.org/10.1109/icse.2007.77openalex-snapshot
Software Development Environments for Scientific and Engineering Software: A Series of Case Studies
inferredcites →https://doi.org/10.1109/mc.1987.1663532openalex-snapshot
No Silver Bullet Essence and Accidents of Software Engineering
inferredcites →https://doi.org/10.1109/mcse.2009.129openalex-snapshot
The Promises of Functional Programming
inferredcites →https://doi.org/10.1109/mcse.2009.205openalex-snapshot
Scientific Computing's Productivity Gridlock: How Software Engineering Can Help
inferredcites →https://doi.org/10.1109/micro.2007.4408246openalex-snapshot
Revisiting the Sequential Programming Model for Multi-Core
inferredcites →https://doi.org/10.1109/ms.2008.103openalex-snapshot
Understanding the High-Performance-Computing Community: A Software Engineer's Perspective
inferredcites →https://doi.org/10.1109/saner.2016.108openalex-snapshot
Modern Release Engineering in a Nutshell -- Why Researchers Should Care
inferredcites →https://doi.org/10.1109/sc.2000.10001openalex-snapshot
MPI versus MPI+OpenMP on the IBM SP for the NAS Benchmarks
inferredcites →https://doi.org/10.1109/sc.2005.53openalex-snapshot
Parallel Programmer Productivity: A Case Study of Novice Parallel Programmers
inferredcites →https://doi.org/10.1109/sc.2012.113openalex-snapshot
What scientific applications can benefit from hardware transactional memory?
inferredcites →https://doi.org/10.1109/secse.2009.5069155openalex-snapshot
How do scientists develop and use scientific software?
inferredcites →https://doi.org/10.1109/tc.1972.5009071openalex-snapshot
Some Computer Organizations and Their Effectiveness
inferredcites →https://doi.org/10.1109/uic-atc-scalcom-cbdcom-iop-smartworld.2016.0098openalex-snapshot
The Weekend Warrior: How to Build a Genomic Supercomputer in Your Spare Time Using Streams and Actors in Scala
inferredcites →https://doi.org/10.1109/vlhcc.2007.17openalex-snapshot
Some Problems of Professional End User Developers
inferredcites →https://doi.org/10.1111/j.1740-9713.2015.00827.xopenalex-snapshot
The Reproducibility Crisis in Science: A Statistical Counterattack
inferredcites →https://doi.org/10.1126/science.1084564openalex-snapshot
The Human Genome Project: Lessons from Large-Scale Biology
inferredcites →https://doi.org/10.1126/science.1213847openalex-snapshot
Reproducible Research in Computational Science
inferredcites →https://doi.org/10.1126/scitranslmed.aaf5027openalex-snapshot
What does research reproducibility mean?
inferredcites →https://doi.org/10.1128/genomea.00403-17openalex-snapshot
Fourteen Draft Genome Sequences for the First Reported Cases of Azithromycin-Resistant Neisseria gonorrhoeae in Ireland
inferredcites →https://doi.org/10.1145/1101815.1101817openalex-snapshot
Impact of software engineering research on the practice of software configuration management
inferredcites →https://doi.org/10.1145/111062.111063openalex-snapshot
Concepts in configuration management systems
inferredcites →https://doi.org/10.1145/1287624.1287679openalex-snapshot
A framework for characterization and analysis of software system scalability
inferredcites →https://doi.org/10.1145/130697.130699openalex-snapshot
Report on the programming language Haskell
inferredcites →https://doi.org/10.1145/1465482.1465560openalex-snapshot
Validity of the single processor approach to achieving large scale computing capabilities
inferredcites →https://doi.org/10.1145/1668862.1668876openalex-snapshot
The history of version control
inferredcites →https://doi.org/10.1145/1852786.1852802openalex-snapshot
A survey of scientific software development
inferredcites →https://doi.org/10.1145/1953611.1953622openalex-snapshot
Mechanisms that separate algorithms from implementations for parallel patterns
inferredcites →https://doi.org/10.1145/2063348.2063374openalex-snapshot
A survey of the practice of computational science
inferredcites →https://doi.org/10.1145/2460276.2462076openalex-snapshot
Eventual Consistency Today: Limitations, Extensions, and Beyond
inferredcites →https://doi.org/10.1145/2675743.2771880openalex-snapshot
Reactive stream processing for data-centric publish/subscribe
inferredcites →https://doi.org/10.1145/2741948.2741964openalex-snapshot
Large-scale cluster management at Google with Borg
inferredcites →https://doi.org/10.1145/2786805.2786850openalex-snapshot
Quality and productivity outcomes relating to continuous integration in GitHub
inferredcites →https://doi.org/10.1145/3293881.3295781openalex-snapshot
Cloud computing: developing contemporary computer science curriculum for a cloud-first future
inferredcites →https://doi.org/10.1145/366663.366704openalex-snapshot
Design of a separable transition-diagram compiler
inferredcites →https://doi.org/10.1145/72551.72554openalex-snapshot
Conception, evolution, and application of functional programming languages
inferredcites →https://doi.org/10.1145/945445.945462openalex-snapshot
Xen and the art of virtualization
inferredcites →https://doi.org/10.1145/974044.974064openalex-snapshot
Exploring architectural scalability
inferredcites →https://doi.org/10.1186/1471-2105-11-s12-s1openalex-snapshot
An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics
inferredcites →https://doi.org/10.1186/1471-2105-7-273openalex-snapshot
Agile methods in biomedical software development: a multi-site experience report
inferredcites →https://doi.org/10.1186/1471-2164-11-s4-s27openalex-snapshot
Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi)
inferredcites →https://doi.org/10.1186/gb-2008-9-12-114openalex-snapshot
Bioinformatics: alive and kicking
inferredcites →https://doi.org/10.1186/gb-2009-10-11-r134openalex-snapshot
Searching for SNPs with cloud computing
inferredcites →https://doi.org/10.1186/gb-2010-11-8-r83openalex-snapshot
Cloud-scale RNA-sequencing differential expression analysis with Myrna
inferredcites →https://doi.org/10.1186/s12859-016-1062-1openalex-snapshot
QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics
inferredcites →https://doi.org/10.1186/s12859-017-1747-0openalex-snapshot
Investigating reproducibility and tracking provenance – A genomic workflow case study
inferredcites →https://doi.org/10.1186/s12918-016-0288-xopenalex-snapshot
Where next for the reproducibility agenda in computational biology?
inferredcites →https://doi.org/10.1186/s13742-015-0092-3openalex-snapshot
Enhanced reproducibility of SADI web service workflows with Galaxy and Docker
inferredcites →https://doi.org/10.1214/09-aoas291openalex-snapshot
Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology
inferredcites →https://doi.org/10.12688/f1000research.7536.1openalex-snapshot
BioShaDock: a community driven bioinformatics shared Docker-based tools registry
inferredcites →https://doi.org/10.1371/journal.pbio.2002050openalex-snapshot
All biology is computational biology
inferredcites →https://doi.org/10.1371/journal.pcbi.0020087openalex-snapshot
Scientific Software Development Is Not an Oxymoron
inferredcites →https://doi.org/10.1371/journal.pcbi.1002021openalex-snapshot
The Roots of Bioinformatics in Theoretical Biology
inferredcites →https://doi.org/10.1371/journal.pcbi.1002487openalex-snapshot
Rise and Demise of Bioinformatics? Promise and Progress
inferredcites →https://doi.org/10.1371/journal.pcbi.1003285openalex-snapshot
Ten Simple Rules for Reproducible Computational Research
inferredcites →https://doi.org/10.1371/journal.pcbi.1005412openalex-snapshot
Ten simple rules for making research software more robust
inferredcites →https://doi.org/10.1371/journal.pmed.0020124openalex-snapshot
Why Most Published Research Findings Are False
inferredcites →https://doi.org/10.14778/2824032.2824063openalex-snapshot
Building a replicated logging system with Apache Kafka
inferredcites →https://doi.org/10.3389/fgene.2019.00356openalex-snapshot
Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis
inferredcites →https://doi.org/10.4230/oasics.microservices.2020-2022.5openalex-snapshot
Cloud Programming Simplified: A Berkeley View on Serverless Computing
inferredcites →https://doi.org/10.6028/nist.sp.800-145openalex-snapshot
The NIST definition of cloud computing
inferredcites →https://doi.org/10.7717/peerj-cs.85openalex-snapshot
GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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